The Quantum theory of atoms in molecules : from solid state to DNA and drug design

Foreword. Preface. List of Abbreviations Appearing in this Volume. List of Contributors. 1 An Introduction to the Quantum Theory of Atoms in Molecules (Cherif F. Matta and Russell J. Boyd). 1.1 Introduction. 1.2 The Topology of the Electron Density. 1.3 The Topology of the Electron Density Dictates the Form of Atoms in Molecules. 1.4 The Bond and Virial Paths, and the Molecular and Virial Graphs. 1.5 The Atomic Partitioning of Molecular Properties. 1.6 The Nodal Surface in the Laplacian as the Reactive Surface of a Molecule. 1.7 Bond Properties. 1.8 Atomic Properties. 1.9 "Practical" Uses and Utility of QTAIM Bond and Atomic Properties. 1.10 Steps of a Typical QTAIM Calculation. References. Part I Advances in Theory. 2 The Lagrangian Approach to Chemistry (Richard F. W. Bader). 2.1 Introduction. 2.2 The Lagrangian Approach. 2.3 The Action Principle in Quantum Mechanics. 2.4 From Schrodinger to Schwinger. 2.5 Molecular Structure and Structural Stability. 2.6 Re.ections and the Future. References. 3 Atomic Response Properties (Todd A. Keith). 3.1 Introduction. 3.2 Apparent Origin-dependence of Some Atomic Response Properties. 3.3 Bond Contributions to "Null" Molecular Properties. 3.4 Bond Contributions to Atomic Charges in Neutral Molecules. 3.5 Atomic Contributions to Electric Dipole Moments of Neutral Molecules. 3.6 Atomic Contributions to Electric Polarizabilities. 3.7 Atomic Contributions to Vibrational Infrared Absorption Intensities. 3.8 Atomic Nuclear Virial Energies. 3.9 Atomic Contributions to Induced Electronic Magnetic Dipole Moments. 3.10 Atomic Contributions to Magnetizabilities of Closed-Shell Molecules. References. 4 QTAIM Analysis of Raman Scattering Intensities: Insights into the Relationship Between Molecular Structure and Electronic Charge Flow (Kathleen M. Gough, Richard Dawes, Jason R. Dwyer, and Tammy L. Welshman). 4.1 Introduction. 4.2 Background to the Problem. 4.3 Methodology. 4.4 Speci.c Examples of the Use of AIM2000 Software to Analyze Raman Intensities. 4.5 Patterns in alpha That Are Discovered Through QTAIM. 4.6 Patterns in qa/qrCH That Apply Across Di.erent Structures, Conformations, Molecular Types: What is Transferable? 4.7 What Can We Deduce From Simple Inspection of &delta &alpha /&delta rCH and &delta &alpha /&delta rCC From Gaussian? 4.8 Conclusion. References. 5 Topological Atom-Atom Partitioning of Molecular Exchange Energy and its Multipolar Convergence (Michel Rafat and Paul L. A. Popelier). 5.1 Introduction. 5.2 Theoretical Background. 5.3 Details of Calculations. 5.4 Results and Discussion. 5.5 Conclusion. References. 6 The ELF Topological Analysis Contribution to Conceptual Chemistry and Phenomenological Models (Bernard Silvi and Ronald J. Gillespie). 6.1 Introduction. 6.2 Why ELF and What is ELF? 6.3 Concepts from the ELF Topology. 6.4 VSEPR Electron Domains and the Volume of ELF Basins. 6.5 Examples of the Correspondence Between ELF Basins and the Domains of the VSEPR Model. 6.6 Conclusions. References. Part II Solid State and Surfaces. 7 Solid State Applications of QTAIM and the Source Function - Molecular Crystals, Surfaces, Host-Guest Systems and Molecular Complexes (Carlo Gatti). 7.1 Introduction. 7.2 QTAIM Applied to Solids - the TOPOND Package. 7.3 QTAIM Applied to Molecular Crystals. 7.4 QTAIM Applied to Surfaces. 7.5 QTAIM Applied to Host-Guest Systems. 7.6 The Source Function: Theory. References. 8 Topology and Properties of the Electron Density in Solids (Victor Luana, Miguel A. Blanco, Aurora Costales, Paula Mori-Sanchez, and Angel Martin Pendas). 8.1 Introduction. 8.2 The Electron Density Topology and the Atomic Basin Shape. 8.3 Crystalline Isostructural Families and Topological Polymorphism. 8.4 Topological Classi.cation of Crystals. 8.5 Bond Properties - Continuity from the Molecular to the Crystalline Regime. 8.6 Basin Partition of the Thermodynamic Properties. 8.7 Obtaining the Electron Density of Crystals. References. 9 Atoms in Molecules Theory for Exploring the Nature of the Active Sites on Surfaces (Yosslen Aray, Jesus Rodriguez, and David Vega). 9.1 Introduction. 9.2 Implementing the Determination of the Topological Properties of p(r) from a Three-dimensional Grid. 9.3 An Application to Nanocatalyts - Exploring the Structure of the Hydrodesulfurization MoS2 Catalysts. References. Part III Experimental Electron Densities and Biological Molecules. 10 Interpretation of Experimental Electron Densities by Combination of the QTAMC and DFT (Vladimir G. Tsirelson). 10.1 Introduction. 10.2 Specificity of the Experimental Electron Density. 10.3 Approximate Electronic Energy Densities. 10.4 The Integrated Energy Quantities. 10.5 Concluding Remarks. References. 11 Topological Analysis of Proteins as Derived from Medium and Highresolution Electron Density: Applications to Electrostatic Properties (Laurence Leherte, Benoit Guillot, Daniel P. Vercauteren, Virginie Pichon-Pesme, Christian Jelsch, Ange'lique Lagoutte, and Claude Lecomte). 11.1 Introduction. 11.2 Methodology and Technical Details. 11.3 Topological Properties of Multipolar Electron Density Database. 11.4 Analysis of Local Maxima in Experimental and Promolecular Mediumresolution Electron Density Distributions. 11.5 Calculation of Electrostatic Properties from Atomic and Fragment Representations of Human Aldose Reductase. 11.6 Conclusions and Perspectives. References. 12 Fragment Transferability Studied Theoretically and Experimentally with QTAIM - Implications for Electron Density and Invariom Modeling (Peter Luger and Birger Dittrich). 12.1 Introduction. 12.2 Experimental Electron-density Studies. 12.3 Studying Transferability with QTAIM - Atomic and Bond Topological Properties of Amino Acids and Oligopeptides. 12.4 Invariom Modeling. 12.5 Applications of Aspherical Invariom Scattering Factors. 12.6 Conclusion. References. Part IV Chemical Bonding and Reactivity. 13 Interactions Involving Metals - From "Chemical Categories" to QTAIM, and Backwards (Piero Macchi and Angelo Sironi). 13.1 Introduction. 13.2 The Electron Density in Isolated Metal Atoms - Hints of Anomalies. 13.3 Two-center Bonding. 13.4 Three-center Bonding. 13.5 Concluding Remarks. References. 14 Applications of the Quantum Theory of Atoms in Molecules in Organic Chemistry - Charge Distribution, Conformational Analysis and Molecular Interactions (Jesus Hernandez-Trujillo, Fernando Cortes-Guzman, and Gabriel Cuevas). 14.1 Introduction. 14.2 Electron Delocalization. 14.3 Conformational Equilibria. 14.4 Aromatic Molecules. References. 15 Aromaticity Analysis by Means of the Quantum Theory of Atoms in Molecules (Eduard Matito, Jordi Poater, and Miquel Sola ). 15.1 Introduction. 15.2 The Fermi Hole and the Delocalization Index. 15.3 Electron Delocalization in Aromatic Systems. 15.4 Aromaticity Electronic Criteria Based on QTAIM. 15.5 Applications of QTAIM to Aromaticity Analysis. 15.6 Conclusions. References. 16 Topological Properties of the Electron Distribution in Hydrogen-bonded Systems (Ignasi Mata, Ibon Alkorta, Enrique Espinosa, Elies Molins, and Jose Elguero). 16.1 Introduction. 16.2 Topological Properties of the Hydrogen Bond. 16.3 Energy Properties at the Bond Critical Point (BCP). 16.4 Topological Properties and Interaction Energy. 16.5 Electron Localization Function, n(r). 16.6 Complete Interaction Range. 16.7 Concluding Remarks. References. 17 Relationships between QTAIM and the Decomposition of the Interaction Energy - Comparison of Different Kinds of Hydrogen Bond (Stawomir J. Grabowski). 17.1 Introduction. 17.2 Diversity of Hydrogen-bonding Interactions. 17.3 The Decomposition of the Interaction Energy. 17.4 Relationships between the Topological and Energy Properties of Hydrogen Bonds. 17.5 Various Other Interactions Related to Hydrogen Bonds. 17.6 Summary. References. Part V Application to Biological Sciences and Drug Design. 18 QTAIM in Drug Discovery and Protein Modeling (Nagamani Sukumar and Curt M. Breneman). 18.1 QSAR and Drug Discovery. 18.2 Electron Density as the Basic Variable. 18.3 Atom Typing Scheme and Generation of the Transferable Atom Equivalent (TAE) Library. 18.4 TAE Reconstruction and Descriptor Generation. 18.5 QTAIM-based Descriptors. 18.6 Sample Applications. 18.7 Conclusions. References. 19 Fleshing-out Pharmacophores with Volume Rendering of the Laplacian of the Charge Density and Hyperwall Visualization Technology (Preston J. MacDougall and Christopher E. Henze). 19.1 Introduction. 19.2 Computational and Visualization Methods. 19.3 Subatomic Pharmacophore Insights. 19.4 Conclusion. References. Index.